Strain identifier

BacDive ID: 139548

Type strain: Yes

Species: Allorhizobium vitis

Strain Designation: K309

Strain history: CIP <- 1999, C. Marshall, CSL, York, UK <- K. Ophel <- 1988, A. Kerr: strain K309

NCBI tax ID(s): 1265506 (strain), 373 (species)

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General

@ref: 41916

BacDive-ID: 139548

keywords: genome sequence, Bacteria, mesophilic, Gram-negative, rod-shaped

description: Allorhizobium vitis K309 is a mesophilic, Gram-negative, rod-shaped bacterium of the family Rhizobiaceae.

NCBI tax id

NCBI tax idMatching level
1265506strain
373species

strain history

  • @ref: 41916
  • history: CIP <- 1999, C. Marshall, CSL, York, UK <- K. Ophel <- 1988, A. Kerr: strain K309

doi: 10.13145/bacdive139548.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Rhizobiaceae
  • genus: Allorhizobium
  • species: Allorhizobium vitis
  • full scientific name: Allorhizobium vitis (Ophel and Kerr 1990) Mousavi et al. 2016

  • synonyms

    @refsynonym
    20215Rhizobium vitis
    20215Allorhizobium vitis
    20215Agrobacterium vitis

@ref: 41916

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Rhizobiaceae

genus: Allorhizobium

species: Allorhizobium vitis

strain designation: K309

type strain: yes

Morphology

cell morphology

  • @ref: 41916
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 41916

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41916MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
41916CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
41916positivegrowth30mesophilic
41916positivegrowth15-30
41916nogrowth5psychrophilic
41916nogrowth37mesophilic
41916nogrowth41thermophilic
41916nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
41916NaClpositivegrowth0-2 %
41916NaClnogrowth4 %
41916NaClnogrowth6 %
41916NaClnogrowth8 %
41916NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4191616947citrate+carbon source
419164853esculin+hydrolysis
41916606565hippurate+hydrolysis
4191617632nitrate-builds gas from
4191617632nitrate-reduction
4191616301nitrite-builds gas from
4191616301nitrite-reduction
4191615792malonate+assimilation
4191617632nitrate-respiration

antibiotic resistance

  • @ref: 41916
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 41916
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4191615688acetoin-
4191617234glucose-

enzymes

@refvalueactivityec
41916oxidase+
41916beta-galactosidase+3.2.1.23
41916alcohol dehydrogenase-1.1.1.1
41916gelatinase-
41916amylase-
41916DNase-
41916caseinase-3.4.21.50
41916catalase+1.11.1.6
41916tween esterase-
41916gamma-glutamyltransferase+2.3.2.2
41916lecithinase-
41916lipase-
41916lysine decarboxylase-4.1.1.18
41916ornithine decarboxylase-4.1.1.17
41916phenylalanine ammonia-lyase+4.3.1.24
41916protease-
41916tryptophan deaminase-
41916urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
41916-+++-+----++++-+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
41916+++++-+++-++-+++++++++-++++----+++-+++++---+-+--+++--+-++--+--+++-----+----+--+++-----+--++--------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typeisolation date
41916AustraliaAUSAustralia and Oceania
41916AustraliaAUSAustralia and OceaniaGrapevine, vitis vinifera1977

Safety information

risk assessment

  • @ref: 41916
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agrobacterium vitis NCPPB 3554GCA_001541345scaffoldncbi373
66792Agrobacterium vitis strain NCPPB 3554373.9wgspatric373
66792Agrobacterium vitis NCPPB 35542728368991draftimg373

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno68.842no
flagellatedno68.842no
gram-positiveno98.318no
gram-positiveno98.318no
anaerobicno98.597no
anaerobicno98.597no
aerobicyes92.472no
aerobicyes92.472no
halophileno92.774no
halophileno92.774no
spore-formingno94.559no
spore-formingno94.559no
glucose-utilyes93.199no
glucose-utilyes93.199no
motileyes84.121no
motileyes84.121no
thermophileno98.898yes
thermophileno98.898yes
glucose-fermentno88.535no
glucose-fermentno88.535no

External links

@ref: 41916

culture collection no.: CIP 105853, NCPPB 3554, ATCC 49767, ICMP 10752, HAMBI 1817, LMG 8750

straininfo link

  • @ref: 96028
  • straininfo: 687

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics8554768Variability of the 5'-end of the large subunit rDNA and presence of a new short class of rRNA in Rhizobiaceae.Evguenieva-Hackenberg E, Selenska-Pobell SLett Appl Microbiol10.1111/j.1472-765x.1995.tb01092.x1995Base Sequence, Genetic Variation/*genetics, Introns/genetics, Molecular Sequence Data, Molecular Weight, RNA Processing, Post-Transcriptional, RNA, Bacterial/chemistry/*genetics, RNA, Ribosomal, 23S/chemistry/*genetics, Rhizobiaceae/*genetics
Genetics8661947Major differences between the rrnA operons of two strains of Agrobacterium vitis.Otten L, De Ruffray PArch Microbiol10.1007/s0020300503571996Base Sequence, Molecular Sequence Data, RNA, Ribosomal/analysis, Rhizobium/*genetics, *rRNA OperonPhylogeny
Phylogeny27959784Rhizobium oryziradicis sp. nov., isolated from rice roots.Zhao JJ, Zhang J, Sun L, Zhang RJ, Zhang CW, Yin HQ, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0017242017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizobium/*classification/genetics/isolation & purification, Sequence Analysis, DNATranscriptome
Genetics30533933High-Quality Draft Genome Sequence of the Type Strain of Allorhizobium vitis, the Primary Causal Agent of Grapevine Crown Gall.Gan HM, Lee MVJ, Savka MAMicrobiol Resour Announc10.1128/MRA.01045-182018

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
41916Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105853Collection of Institut Pasteur (CIP 105853)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68382Automatically annotated from API zym
96028Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID687.1